Dimer Formation Research Articles

The MUC2 Gene Product: Polymerisation and Post-Secretory Organisation-Current Models.

MUC2 mucin, the primary gel-forming component of intestinal mucus, is well researched and a model of polymerisation and post-secretory organisation has been published previously. Recently, several significant developments have been made which either introduce new ideas or challenge previous theories. New ideas include an overhaul of the MUC2 C-terminal globular structure which is proposed to harbour several previously unobserved domains, and include a site for an extra intermolecular disulphide bridge dimer between the cysteine 4379 of adjacent MUC2 C-termini. MUC2 polymers are also now thought to be secreted attached to the epithelial surface of goblet cells in the small intestine and removed following secretion via a metalloprotease meprin β-mediated cleavage of the von Willebrand D2 domain of the N-terminus. It remains unclear whether MUC2 forms intermolecular dimers, trimers, or both, at the N-termini during polymerisation, with several articles supporting either trimer or dimer formation. The presence of a firm inner mucus layer in the small intestine is similarly unclear. Considering this recent research, this review proposes an update to the previous model of MUC2 polymerisation and secretion, considers conflicting theories and data, and highlights the importance of this research to the understanding of MUC2 mucus layers in health and disease.

Testing the Simplified Molecular Dynamics Approach to Improve the Reproduction of ECD Spectra and Monitor Aggregation.

A simplified molecular-dynamics-based electronic circular dichroism (ECD) approach was tested on three condensed derivatives with limited conformational flexibility and an isochroman-2H-chromene hybrid, the ECD spectra of which could not be precisely reproduced by the conventional ECD calculation protocol. Application of explicit solvent molecules at the molecular mechanics (MD) level in the dynamics simulations and subsequent TDDFT-ECD calculation for the unoptimized MD structures was able to improve the agreements between experimental and computed spectra. Since enhancements were achieved even for molecules with limited conformational flexibility, deformations caused by the solvent molecules and multitudes of conformers produced with unoptimized geometries seem to be key factors for better agreement. The MD approach could confirm that aggregation of the phenanthrene natural product luzulin A had a significant contribution to a specific wavelength range of the experimental ECD. The MD approach has proved that dimer formation occurred in solution and this was responsible for the anomalous ECD spectrum. The scope and limitations of the method have also been discussed.

AKT1 Promotes Tumorigenesis and Metastasis by Directly Phosphorylating Hexokinases.

The importance of protein kinase B (AKT) in tumorigenesis and development is well established, but its potential regulation of metabolic reprogramming via phosphorylation of the hexokinase (HK) isozymes remains unclear. There are two HK family members (HK1/2) and three AKT family members (AKT1/2/3), with varied distribution of AKTs exhibiting distinct functions in different tissues and cell types. Although AKT is known to phosphorylate HK2 at threonine 473, AKT-mediated phosphorylation of HK1 has not been reported. We examined direct binding and phosphorylation of HK1/2 by AKT1 and identified the phosphorylation modification sites using coimmunoprecipitation, glutathione pull-down, western blotting, and in vitro kinase assays. Regulation of HK activity through phosphorylation by AKT1 was also examined. Uptake of 2-[1,2-3H]-deoxyglucose and production of lactate were investigated to determine whether AKT1 regulates glucose metabolism by phosphorylating HK1/2. Functional assays, immunohistochemistry, and tumor experiments in mice were performed to investigate whether AKT1-mediated regulation of tumor development is dependent on its kinase activity and/or the involvement of HK1/2. AKT interacted with and phosphorylated HK1 and HK2. Serine phosphorylation significantly increased AKT kinase activity, thereby enhancing glycolysis. Mechanistically, the phosphorylation of HK1 at serine 178 (S178) by AKT significantly decreased the Km and enhanced the Vmax by interfering with the formation of HK1 dimers. Mutations in the AKT phosphorylation sites of HK1 or HK2 significantly abrogated the stimulatory characteristics of AKT on glycolysis, tumorigenesis, and cell migration, invasion, proliferation, and metastasis. HK1-S178 phosphorylation levels were significantly correlated with the occurrence and metastasis of different types of clinical tumors. We conclude that AKT not only regulates tumor glucose metabolism by directly phosphorylating HK1 and HK2, but also plays important roles in tumor progression, proliferation, and migration.

A novel dimer induced AIE smart material for fluorescence colorimetric detection of food freshness and Zn2+

A simple, smart material (2-(benzo[d]thiazol-2-yl)-4-hydroxy-7-methylphthalazin-1(2H)-one, BTHM) have been developed by one-step reaction, which displayed an aggregation-induced emission (AIE) effect because of due to the unique dimer formation by intermolecular hydrogen bonds by XRD measurements. BTHM exhibited strong solid-state emission and is sensitive to Et3N/CH2Cl2 vapor stimulus and could be used as a portable test strip for identifying different concentrations of Et3N/CH2Cl2 vapor. Also, it successfully realized blue/green luminescence switching by the external Et3N/AcOH vapor stimuli with a high repeatability. BTHM labels have been preferentially used for real-time and visual monitoring of the freshness of the pork and shrimp food. Also, the BTHM display fluorescence colorimetric response to Zn2+ in EtOH/H2O (1/9, V/V, pH=7.4) medium with high selectivity and sensitivity. Importantly, BTHM could be used to monitor Zn2+ in living A549 cells by an outstanding fluorescence color signal change. Further, the theoretical calculations have been performed to address the sensing mechanism.

Atomic rare earths activate direct O-O coupling in manganese oxide towards electrocatalytic oxygen evolution

Activating the efficient electron transfer in oxygen evolution reaction (OER) by tuning the oxygen (O) electronic states near the Fermi level is essential to break the linear scaling limitation of OER intermediates. Herein, we construct a series of rare earth (RE) single atoms on MnO2 nanosheets with modulated oxygen states by an effective and universal Ar plasma (P)-assisted strategy (P-RE SAs@MnO2, RE = Gd, La, Ce, Tm, and Lu) to investigate the origin of RE-enhanced OER performance. Taking P-Gd SAs@MnO2 as a representative, the atomically dispersed Gd atoms on MnO2 assist the construction of localized asymmetric [Gd−O−Mn] units, which induces electron accumulation at surrounding oxygen sites by introducing the polarized ionic Gd−O bond. As a result, the P-Gd SAs@MnO2 delivers impressive OER performance with low overpotential (281 mV@10 mA cm −2; ηj10), robust long-term stability, and optimized activation energy (Ea = 32.07 kJ mol−1 at ηj10), which are superior to RE-free MnO2, commercial RuO2, and most Mn-based catalysts. Similar enhanced OER performance can also be found for other P-RE SAs@MnO2 (RE = La, Ce, Tm, and Lu). X-ray absorption and in situ Raman spectroscopy unveil the preferred electron accumulation at Mn−O, promoting the formation of terminal MnIV=O intermediates in OER. Theoretical calculations demonstrate that the construction of [Gd−O−Mn] unit endows the surface lattice unsaturated O site with the labile property, which assists the direct formation of (O−O) dimer for circumventing the universal scaling relation applied by the formation of *OOH. This work opens up a new avenue for the design of transition metal oxides with modulated oxygen state to break the limitation of the adsorbate evolution mechanism during OER.

ТЕСТ-СИСТЕМА ДЛЯ ПРОВЕДЕНИЯ ПЦР В РЕЖИМЕ РЕАЛЬНОГО ВРЕМЕНИ ДЛЯ ОБНАРУЖЕНИЯ ДНК ТТV В БИОЛОГИЧЕСКОМ МАТЕРИАЛЕ

Background. The study of biological material for the presence of TTV DNA using the PCR method allows for a timely assessment of the functional state of the human liver and immune system. Objective. To develop components for real-time PCR for TTV DNA detection in biological material. Material and methods. The design and selection of optimal primers and probes (taking into account the size (length) of the amplicon, annealing temperature, nucleotide composition, distribution of nucleotides along the length of the primer, length of primers, the possibility of formation of hairpins and dimers by primers) were performed using the Primer-BLAST/Primer3, FastPCR programs. Since primers, even absolutely unique for certain DNA sequences, could anneal at nonspecific sites, not related to the gene analyzed, we checked the correspondence of the primers to the sequences of the target gene. For this purpose, we used the NCBI Primer BLAST online service and assessed the local pairwise alignment of each primer with all nucleotide sequences of the Refseq databases. Results. As the result of studies carried out on the selection of the optimal primer annealing temperature, primer concentrations, as well as the selection of the optimal nucleotide pair, the main parameters of the designed primers were determined. Conclusions. A kit for the detection and quantification of TTV DNA using the polymerase chain reaction method with hybridization-fluorescent detection in real time was created and became the basis for the development of a commercial test system.

Adsorption of dimethylaluminum isopropoxide (DMAI) on the Al2O3 surface: A machine-learning potential study

Dimethylaluminum isopropoxide (DMAI) is attracting attention as an alternative precursor for atomic layer deposition (ALD) of aluminum oxide (Al2O3). However, the surface chemical reaction mechanisms of DMAI during ALD regarding its dimeric structure under vacuum deposition process conditions has yet to be clear. In this work, the adsorption mechanism of dimeric and monomeric DMAI on a fully hydroxylated Al2O3 surface is studied using machine-learning potential (MLP) calculations. The initial adsorption of DMAI appears facile and would result in the coexistence of both methyl and isopropoxy ligands on the surface. The reactivity of DMAI is smaller than that of TMA, owing to the propensity of DMAI to adopt a dimeric form. Especially when the substrate is partially covered by other adsorbate species, the large molecular size and low reactivity of dimeric DMAI considerably hinder its reactivity toward surface adsorption. Current results are in good correspondence with the previous experimental results, where lower growth per cycle (GPC) and higher selectivity in area-selective ALD (AS-ALD) could be observed by using DMAI than compared to those of TMA processes.

Simulating the Lyotropic Phase Behavior of a Partially Self-Complementary DNA Tetramer.

DNA oligomers in solution have been found to develop liquid crystal phases via a hierarchical process that involves Watson-Crick base pairing, supramolecular assembly into columns of duplexes, and long-range ordering. The multiscale nature of this phenomenon makes it difficult to quantitatively describe and assess the importance of the various contributions, particularly for very short strands. We performed molecular dynamics simulations based on the coarse-grained oxDNA model, aiming to depict all of the assembly processes involved and the phase behavior of solutions of the DNA GCCG tetramers. We find good quantitative matching to experimental data at both levels of molecular association (thermal melting) and collective ordering (phase diagram). We characterize the isotropic state and the low-density nematic and high-density columnar liquid crystal phases in terms of molecular order, size of aggregates, and structure, together with their effects on diffusivity processes. We observe a cooperative aggregation mechanism in which the formation of dimers is less thermodynamically favored than the formation of longer aggregates.

A phase 1/2, first-in-human, open-label, dose-escalation study of TAK-280, an investigational B7-H3 x CD3ε conditional bispecific redirected activation (COBRA) T-cell engager, in adult patients with unresectable, locally advanced, or metastatic solid tumors.

TPS2684 Background: TAK-280 is a novel COBRA T-cell engager that targets the B7 homolog 3 protein (B7-H3), an antigen highly expressed in a range of solid tumors including metastatic castration-resistant prostate cancer (mCRPC) and non–small cell lung cancer. In its prodrug form, TAK-280 binds to B7-H3, but not to CD3ε. Once in the protease-rich tumor microenvironment, TAK-280 undergoes protease-mediated activation through formation of CD3ε-binding active dimers, which stimulate CD3 T-cell activation and cytotoxic antitumor response against co-engaged B7-H3–expressing cells. In preclinical studies, TAK-280 demonstrated cleavage-dependent conditionality, engagement of tumor target antigen, and induction of T-cell mediated tumor killing. TAK-280 has the potential to target solid tumors that are not amenable to treatment with conventional first- or second-generation T-cell engagers, while limiting toxicity to normal tissues. Methods: This phase 1/2 study is enrolling adult patients with unresectable, locally advanced, or metastatic solid tumors described in the literature to have enhanced B7-H3 expression, who are ineligible or intolerant to standard therapies. Other eligibility criteria include Eastern Cooperative Oncology Group performance status ≤1 and measurable disease per RECIST v1.1. Key exclusion criteria include history of autoimmune disease, major surgery ≤8 weeks before first dose of TAK-280, and history of clinically significant cardiac or gastrointestinal disorders. During phase 1 dose escalation, TAK-280 is administered as an intravenous infusion, once weekly, in 28-day cycles at a pre-defined dose level range. Patients who do not experience dose-limiting or other unacceptable toxicities may receive up to 14 treatment cycles depending on response; patients are treated until disease progression, unacceptable toxicity, or withdrawal from study. The dose-escalation phase will determine two recommended doses for expansion to be assessed during the cohort-expansion phase. The primary endpoint is incidence of dose-limiting or other toxicities during dose escalation; secondary endpoints include pharmacokinetic parameters, response assessment per RECIST v1.1, overall response rate, duration of response, progression-free survival, overall survival, disease control rate, and prostate-specific antigen response in patients with mCRPC. Cytokine release syndrome is closely managed and reported per American Society for Transplantation and Cellular Therapy consensus grading. Approximately 182 patients are planned to be enrolled (42 in dose escalation and 100–142 in cohort-expansion); as of the data cutoff date of Jan 10, 2024, 18 patients have received the study drug. Clinical trial information: NCT05220098 .

Matrix Effect on Singlet Oxygen Generation Using Methylene Blue as Photosensitizer

Methylene blue (MB) is a well-established and extensively studied photosensitizer for photodynamic therapy (PDT), since it can generate singlet oxygen with a high quantum yield upon irradiation within the phototherapeutic (600–950 nm) window. However, its activity can decrease due to the formation of dimers or higher aggregates, which can take place in an aqueous solution at relatively high concentrations. The incorporation of this molecule into a matrix can avoid this aggregation and increase its activity relative to PDT. Silica porous nanoparticles are chosen here as a matrix to host MB. The size and pore geometry are tuned in order to decrease MB leaching while maintaining good singlet oxygen generation and colloidal stability for further applications in nanomedicine. In addition, phenyl functions are grafted on the pores of the silica matrix in order to avoid MB aggregation, thereby increasing the activity of the photosensitizer in the singlet oxygen generation. DFT calculations give insight in the structure of the aggregation of the MB units, and the roles of water and organic environments are investigated through time-dependent calculations on UV-vis spectra.

Targeting an Old Foe for Cancer: A Molecular Dynamics Perspective to Unravel the Specific Binding Nature of 2-Methoxy Estradiol to Human β-Tubulin Isotypes.

Microtubules, composed of α- and β-tubulin subunits are crucial for cell division with their dynamic tissue-specificity which is dictated by expression of isotypes. These isotypes differ in carboxy-terminal tails (CTTs), rich in negatively charged acidic residues in addition to the differences in the composition of active site residues. 2-Methoxy estradiol (2-ME) is the first antimicrotubule agent that showed less affinity toward hemopoietic-specific β1 isotype consequently preventing myelosuppression toxicity. The present study focuses on the MD-directed conformational analysis of 2-ME and estimation of its binding affinity in the colchicine binding pocket of various β-tubulin isotypes combined with the α-tubulin isotype, α1B. AlphaFold 2.0 was used to predict the 3D structure of phylogenetically divergent human β-tubulin isotypes in dimer form with α1B. The dimeric complexes were subjected to induced-fit docking with 2-ME. The statistical analysis of docking showed differences in the binding characteristics of 2-ME with different isotypes. The replicas of atom-based molecular dynamic simulations of the best conformation of 2-ME provided insights into the molecular-level details of its binding pattern across the isotypes. Furthermore, the MM/GBSA analyses revealed the specific binding energy profile of 2-ME in β-tubulin isotypes. It also highlighed, 2-ME exhibits the lowest binding affinity toward the β1 isotype as supported by experimental study. The present study may offer useful information for designing next-generation antimicrotubule agents that are more specific and less toxic.

The effect of oxidative degradation of Dopa-melanin on its basic physicochemical properties and photoreactivity.

Melanin, particularly eumelanin, is commonly viewed as an efficient antioxidant and photoprotective pigment. Nonetheless, the ability of melanin to photogenerate reactive oxygen species and sensitize the formation of cyclobutane pyrimidine dimers may contribute to melanin-dependent phototoxicity. The phototoxic potential of melanin depends on a variety of factors, including molecular composition, redox state, and degree of aggregation. Using complementary spectroscopic and analytical methods we analyzed the physicochemical properties of Dopa-melanin, a synthetic model of eumelanin, subjected to oxidative degradation induced by aerobic photolysis or exposure to 0.1 M hydrogen peroxide. Both modes of oxidative degradation were accompanied by dose-dependent bleaching of melanin and irreversible modifications of its paramagnetic, ion- and electron-exchange and antioxidant properties. Bleached melanin exhibited enhanced efficiency to photogenerate singlet oxygen in both UVA and short-wavelength visible light. Although chemical changes of melanin subunits, including a relative increase of DHICA content and disruption of melanin polymer induced by oxidative degradation were considered, these two mechanisms may not be sufficient for a satisfactory explanation of the elevated photosensitizing ability of the bleached eumelanin. This study points out possible adverse changes in the photoprotective and antioxidant properties of eumelanin that could occur in pigmented tissues after exposure to high doses of intense solar radiation.

Ca2+ binding shifts dimeric dual oxidase's truncated EF-hand domain to monomer

Hydrogen peroxide, produced by Dual Oxidase (Duox), is essential for thyroid hormone synthesis. Duox activation involves Ca2+ binding to its EF-hand Domain (EFD), which contains two EF-hands (EFs). In this study, we characterized a truncated EFD using spectrometry, calorimetry, electrophoretic mobility, and gel filtration to obtain its Ca2+ binding thermodynamic and kinetics, as well as to assess the associated conformational changes. Our results revealed that its 2nd EF-hand (EF2) exhibits a strong exothermic Ca2+ binding (Ka = 107 M−1) while EF1 shows a weaker binding (Ka = 105 M−1), resulting in the burial of its negatively charged residues. The Ca2+ binding to EFD results in a stable structure with a melting temperature shifting from 67 to 99 °C and induces a structural transition from a dimeric to monomeric form. EF2 appears to play a role in dimer formation in its apo form, while the hydrophobic exposure of Ca2+-bound-EF1 is crucial for dimer formation in its holo form. The result is consistent with structures obtained from Cryo-EM, indicating that a stable structure of EFD with hydrophobic patches upon Ca2+ binding is vital for its Duox's domain-domain interaction for electron transfer.

Neutrophil extracellular trap-induced ferroptosis promotes abdominal aortic aneurysm formation via SLC25A11-mediated depletion of mitochondrial glutathione

BackgroundNeutrophil extracellular traps (NETs) induce oxidative stress, which may initiate ferroptosis, an iron-dependent programmed cell death, during abdominal aortic aneurysm (AAA) formation. Mitochondria regulate the progression of ferroptosis, which is characterized by the depletion of mitochondrial glutathione (mitoGSH) levels. However, the mechanisms are poorly understood. This study examined the role of mitoGSH in regulating NET-induced ferroptosis of smooth muscle cells (SMCs) during AAA formation. MethodsConcentrations of NET markers were tested in plasma samples. Western blotting and immunofluorescent staining were performed to detect the expression and localization of NET and ferroptosis markers in tissue samples. The role of NETs and SMC ferroptosis during AAA formation was investigated using peptidyl arginine deiminase 4 gene (Padi4) knockout or treatment with a PAD4 inhibitor, ferroptosis inhibitor or activator in an angiotensin II-induced AAA mouse model. The regulatory effect of SLC25A11, a mitochondrial glutathione transporter, on mitoGSH and NET-induced ferroptosis of SMCs was investigated using in vitro and in vivo experiments. Transmission electron microscopy was used to detect mitochondrial damage. Blue native polyacrylamide gel electrophoresis was used to analyze the dimeric and monomeric forms of the protein. ResultsSignificantly elevated levels of NETosis and ferroptosis markers in aortic tissue samples were observed during AAA formation. Specifically, NETs promoted AAA formation by inducing ferroptosis of SMCs. Subsequently, SLC25A11 was identified as a potential biomarker for evaluating the clinical prognosis of patients with AAA. Furthermore, NETs decreased the stability and dimerization of SLC25A11, leading to the depletion of mitoGSH. This depletion induced the ferroptosis of SMCs and promoted AAA formation. ConclusionDuring AAA formation, NETs regulate the stability of the mitochondrial carrier protein SLC25A11, leading to the depletion of mitoGSH and subsequent activation of NET-induced ferroptosis of SMCs. Preventing mitoGSH depletion and ferroptosis in SMCs is a potential strategy for treating AAA.

Critical assessment of popular biomolecular force fields for molecular dynamics simulations of folding and enzymatic activity of main protease of coronavirus SARS-CoV-2

The main cysteine protease (Mpro) of coronavirus SARS-CoV-2 has become a promising target for computational development in anti-COVID-19 treatments. Here, we benchmarked the performance of six biomolecular molecular dynamics (MD) force fields (OPLS-AA, CHARMM27, CHARMM36, AMBER03, AMBER14SB and GROMOS G54A7) and three water models (TIP3P, TIP4P and SPC) for reproducing the native fold and the enzymatic activity of Mpro as monomeric and dimeric units. The MD sampling up to 1 μs suggested that the proper choice of the force fields and water models plays an essential role in reproducing the tertiary structure and the inter-residue distance between the catalytic dyad His41-Cys145. We found that while most benchmarked all-atom force fields reproduce well the native fold of Mpro, the CHARMM27/TIP3P and OPLS-AA/TIP4P setups revealed a good performance in reproducing the structure of the catalytic domain. In addition, these FF setups were also well-adopted for MD sampling of Mpro at the physiologic conditions by mimicking the presence of 100 mM NaCl and the elevated temperature of 310 K. Finally, both FFs were also performed well in reproducing the native fold of Mpro in a dimeric form. Therefore, comparing the preservation of the native fold of Mpro and the stability of its catalytic site architecture, our MD benchmarking suggests that the OPLS-AA/TIP4P and CHARMM27/TIP3P MD setups at the physiologic conditions may be well-suited for rapid in silico screening and developing broad-spectrum anti-coronaviral therapeutic agents.

Acetonitrile real gas phase behavior from quasi-ideal gas to nanodroplets: A microscopical view.

We have applied a recently developed general purpose acetonitrile force field based on first-principles calculations to simulate acetonitrile in the gas phase at different temperatures and densities. These conditions range from nearly ideal to real gas phase behavior and condensation. The molecular dynamics simulation results agree fairly well with the experimental studies available in the literature on the gas samples. The structural analysis of aggregates and their associated interaction energies is examined and related to the early model proposed on molecular association and equilibrium determining the non-ideal behavior. The formation of dimers is mainly responsible for the non-ideal behavior of the gas at very low density, confirming suggested models based on previous experimental studies. However, when the density of the sample rises, the level of aggregation increases and the simple concept of dimerization does not hold anymore. The real behavior adopted by the gas is related to the distribution of molecular structures observed. The macroscopical view of a real gas as a generic interparticle interaction system without a defined form may then be rationalized on the basis of a defined molecular association originated by a distribution of aggregates at the low density regime. The sample with the highest density (∼1.4 × 103 molm-3) at the lowest temperature exhibits a massive aggregation where most of the acetonitrile (ACN) molecules in the simulation box form a big cluster. Its radial distribution function is similar to that of the liquid ACN. This strongly inhomogeneous distribution in the box can be considered a condensation in the gas phase under specific density-T conditions. This formation opens the door to the potential tuning of its solvent properties as a function of its size in these nanodroplets that in turn are controlled by the density-T conditions.

BSA Binding and Aggregate Formation of a Synthetic Amino Acid with Potential for Promoting Fibroblast Proliferation: An In Silico, CD Spectroscopic, DLS, and Cellular Study.

This study presents the chemical synthesis, purification, and characterization of a novel non-natural synthetic amino acid. The compound was synthesized in solution, purified, and characterized using NMR spectroscopy, polarimetry, and melting point determination. Dynamic Light Scattering (DLS) analysis demonstrated its ability to form aggregates with an average size of 391 nm, extending to the low micrometric size range. Furthermore, cellular biological assays revealed its ability to enhance fibroblast cell growth, highlighting its potential for tissue regenerative applications. Circular dichroism (CD) spectroscopy showed the ability of the synthetic amino acid to bind serum albumins (using bovine serum albumin (BSA) as a model), and CD deconvolution provided insights into the changes in the secondary structures of BSA upon interaction with the amino acid ligand. Additionally, molecular docking using HDOCK software elucidated the most likely binding mode of the ligand inside the BSA structure. We also performed in silico oligomerization of the synthetic compound in order to obtain a model of aggregate to investigate computationally. In more detail, the dimer formation achieved by molecular self-docking showed two distinct poses, corresponding to the lowest and comparable energies, with one pose exhibiting a quasi-coplanar arrangement characterized by a close alignment of two aromatic rings from the synthetic amino acids within the dimer, suggesting the presence of π-π stacking interactions. In contrast, the second pose displayed a non-coplanar configuration, with the aromatic rings oriented in a staggered arrangement, indicating distinct modes of interaction. Both poses were further utilized in the self-docking procedure. Notably, iterative molecular docking of amino acid structures resulted in the formation of higher-order aggregates, with a model of a 512-mer aggregate obtained through self-docking procedures. This model of aggregate presented a cavity capable of hosting therapeutic cargoes and biomolecules, rendering it a potential scaffold for cell adhesion and growth in tissue regenerative applications. Overall, our findings highlight the potential of this synthetic amino acid for tissue regenerative therapeutics and provide valuable insights into its molecular interactions and aggregation behavior.

Supramolecular Assemblies in Mn(II) and Zn(II) Metal–Organic Compounds Involving Phenanthroline and Benzoate: Experimental and Theoretical Studies

Two new Mn(II) and Zn(II) metal–organic compounds of 1,10-phenanthroline and methyl benzoates viz. [Mn(phen)2Cl2]2-ClBzH (1) and [Zn(4-MeBz)2(2-AmPy)2] (2) (where 4-MeBz = 4-methylbenzoate, 2-AmPy = 2-aminopyridine, phen = 1,10-phenanthroline, 2-ClBzH = 2-chlorobenzoic acid) were synthesized and characterized using elemental analysis, TGA, spectroscopic (FTIR, electronic) and single crystal X-ray diffraction techniques. The crystal structure analysis of the compounds revealed the presence of various non-covalent interactions, which provides stability to the crystal structures. The crystal structure analysis of compound 1 revealed the formation of a supramolecular dimer of 2-ClBzH enclathrate within the hexameric host cavity formed by the neighboring monomeric units. Compound 2 is a mononuclear compound of Zn(II) where flexible binding topologies of 4-CH3Bz are observed with the metal center. Moreover, various non-covalent interactions, such as lp(O)-π, lp(Cl)-π, C–H∙∙∙Cl, π-stacking interactions as well as N–H∙∙∙O, C–H∙∙∙O and C–H∙∙∙π hydrogen bonding interactions, are found to be involved in plateauing the molecular self-association of the compounds. The remarkable enclathration of the H-bonded 2-ClBzH dimer into a supramolecular cavity formed by two [Mn(phen)2Cl2] complexes were further studied theoretically using density functional theory (DFT) calculations, the non-covalent interaction (NCI) plot index and quantum theory of atoms in molecules (QTAIM) computational tools. Synergistic effects were also analyzed using molecular electrostatic potential (MEP) surface analysis.

Mechanistic investigation of iron-catalyzed cross-coupling using sterically encumbered β-diketonate ligands

Iron β-diketonate compounds are reported using the hindered 2,6-dimesitylbenzoyl pinacolone (Aracac), which sterically precludes formation of tris-Aracac complexes. Fe(Aracac)2 (1), Fe(Aracac)2Cl (2) were synthesized and characterized using crystallographic, spectroscopic, elemental analysis, and electrochemical techniques. Iron complexes with only one Aracac ligand form dimers [Fe(Aracac)(THF)2]2(μ-OTf)2 (3) and [(Aracac)Fe(μ-mesityl)]2 (4). Complexes 1–4 were evaluated in a Kumada cross-coupling reaction and compared with the parent FeIII(acac)3 complex. Whereas the bis-acac complexes 1 and 2 show only modest activity (∼50 % yield after 60 min), the mono-acac complexes 3 and 4 are nearly as effective as the parent compound (∼90 % yield). DFT computations, in conjunction with catalytic results and electrochemical observations, suggest a catalytic cycle involving an oxidative addition of an aryl-chloride to Fe(II) to produce a high-spin Fe(IV) complex that could alternately be described as a high-spin Fe(II) stabilizing two coordinated organoradicals. These results suggest that a unique aspect of acac as a ligand for this reaction is its ability to support high-spin organoiron complexes, which can provide low-barrier pathways for C–Cl bond cleavage and CC bond formation reactions.

Binding of coagulation factor IXa to procoagulant platelets revisited: Low affinity and interactions with other factors

Binding of activated factor IX (fIXa) to the phosphatidylserine-expressing procoagulant platelets is a critical step in blood coagulation, which is necessary for the membrane-dependent intrinsic tenase complex assembly and factor X activation. However, the nature and parameters of the fIXa binding sites on the procoagulant platelet surface remain unclear. We used flow cytometry to elucidate the quantitative details of the fluorescently labeled fIXa binding to gel-filtered activated platelets. FIXa bound to the procoagulant platelet subpopulation only, with the parameters (maximal number of binding sites at 58900 ± 3400, Kd at 1000 ± 170 nM) similar to binding observed with phospholipid vesicles. No specific high-affinity binding sites for fIXa were detected, and binding proceeded similarly for different methods of procoagulant platelet production (thrombin, thrombin receptor activation peptide, collagen-related peptide, their combinations, or calcium ionophore A23187). Factor VIII, known to form a high affinity complex with fIXa, enhanced fIXa binding to platelets. In contrast, only competition effects were observed for factor X, which binds fIXa with much lower affinity. Unexpectedly, fIXa itself, fIX, and prothrombin also dose-dependently enhance fIXa binding at concentrations below 1000 nM, suggesting the formation of membrane-bound fIXa dimers and fIXa-prothrombin complexes on platelets. These findings provide a novel perspective on the fIXa binding site on procoagulant platelets, which does not have any major differences from pure phospholipid-based model membranes, exhibits inherently low affinity (3–5 orders of magnitude below the physiologically relevant fIXa concentration) but is significantly enhanced by its cofactor VIII, and regulated by previously unknown membrane interactions.